Usage advice:
the only parameters needed are (fasttree_exe, input='<InputFile>' out='<OutputFile>')

parameters that use values are added this way: (fasttree_exe, parameter=value, input='<InputFile>' out='<OutputFile>')
parameters that don't use values are added this way: (fasttree_exe, parameter=True, input='<InputFile>' out='<OutputFile>')

from the command line use 'fasttree.exe -help' or 'fasttree.exe -expert' for more explanation of usage options